[AMBER] TI method with combination of restrained MD in pmemd.cuda of AMBER18

From: <kegohda2kegohda.mx5.canvas.ne.jp>
Date: Wed, 26 Dec 2018 22:11:59 +0900


I have a question on the implementation of TI method with combination of
restrained MD in pmemd.cuda of AMBER18.

The simulation will be based on one step transformation using softcore
potential to invoke alchemical changes in a ligand in a protein complex.
The restrained MD will be carried out with dihedral constraints in the bonds
of the ligand that will alchemically be changed during the simulation.

For this simulation, TI and NMR parameters in AMBER 18 will be set like
timask 1 and 2
scmask 1 and 2
r1 - r4
rk2, rk3

However, I am wondering if this parameter set can be acceptable for the
current pmemd.cuda, because the reference manual on section 18.6.1 in
page-380 says some limitations for pmemd.cuda;

" 4. nmropt > 1 Support is not currently available for nmropt > 1. In
addition for nmropt = 1 only features that do not change the underlying
force field parameters are supported. For example umbrella sampling
restraints are supported as is Jarzynski sampling as well as simulated
annealing functions such as variation of Temp0 with simulation step.
However, varying the VDW parameters with step is not supported."

I would be happy if you could give me any suggestions on my question.

Keigo Gohda

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Received on Wed Dec 26 2018 - 05:30:02 PST
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